2022年深圳市新型冠状病毒Omicron BA.2亚系变异株的分子特征分析  

Molecular Characterization of SARS⁃CoV⁃2 Omicron BA.2 Sub⁃lineages Isolated in Shenzhen,China,During 2022

作　　者：周莎 陈龙[2] 屈雅丽 吕秋莹[4] 张仁利[2] 姚相杰[2] 孟君[2] 张晓敏 吴春利[2] 孙颖 刘慧[2] 魏欣仪 陈建成 李诗敏 朱灿 卢清菊 钟庭珊 陈慧 胡雪婷 陈妙媚 黄小丽 何雅青 ZHOU Sha;CHEN Long;QU Yali;LYU Qiuying;ZHANG Renli;YAO Xiangjie;MENG Jun;ZHANG Xiaomin;WU Chunli;SUN Ying;LIU Hui;WEI Xinyi;CHEN Jiancheng;LI Shimin;ZHU Can;LU Qingju;ZHONG Tingshan;CHNE Hui;HU Xueting;CHEN Miaomei;HUANG Xiaoli;HE Yaqing(School of Public Health,University of South China,Hengyang 421001,China;Institute of Pathogen Biology,Shenzhen Center for Disease Control and Prevention,Shenzhen 518055,China;Department of Epidemiology,School of Public Health,Southern Medical University,Guangzhou 510515,China;Department of Communicable Diseases Control and Prevention,Shenzhen Center for Disease Control and Prevention,Shenzhen 518055,China)

机构地区：[1]南华大学公共卫生学院,衡阳421001 [2]深圳市疾病预防控制中心病原微生物检测所,深圳518055 [3]南方医科大学公共卫生学院流行病学系,广州510515 [4]深圳市疾病预防控制中心传染病预防控制所,深圳518055

出　　处：《病毒学报》2023年第4期923-931,共9页Chinese Journal of Virology

基　　金：深圳市科技创新委员会技术攻关重点项目(项目号:JSGG20200225152648408),题目:基于SARS⁃CoV⁃2冠状病毒表面Spike蛋白的早期快检技术研发;深圳市科技创新委员会技术攻关重点项目(项目号:JSGG20210901145004012),题目:新冠病毒变异株快速检测试剂盒关键技术研发;深圳市科技创新委员会技术攻关重点项目(项目号:JSGG20220606141401003),题目:抗疫专2022055新冠病毒S蛋白抗原自测试纸条及材料关键技术研发。

摘　　要：新型冠状病毒(SARS⁃CoV⁃2)BA.2亚谱系BA.2.12.1表现出令人担忧的传播能力。为了了解深圳本地与输入的BA.2亚谱系分布与遗传特征,本研究对2022年1⁃6月深圳市BA.2亚系变异株进行了全基因组序列分析。通过高通量测序,本研究获得了155例本土、30例输入共185株覆盖度98%以上的BA.2亚型毒株的基因组序列。185株BA.2亚型毒株可分为BA.2.2、BA.2.3、BA.2.9、BA.2.10、BA.2.10.1、BA.2.12.1和BA.2.29七种亚型,其中BA.2.2占比最高(92.97%,172/185),其他亚型占比从高到低依次为BA.2.10.1(2.70%,5/185)、BA.2.10(1.62%,3/185)、BA.2.9(1.08%,2/185)、BA.2.3(0.54%,1/185)、BA.2.12.1(0.54%,1/185)及BA.2.29(0.54%,1/185)。172株BA.2.2亚型变异株中,本土及中国香港输入各153株(88.95%)和19株(11.05%)。序列比较分析发现,153株深圳本土BA.2.2毒株与19株中国香港输入BA.2.2毒株共享69个核苷酸变异位点和52个氨基酸变异位点(不包括缺失突变)。根据单核苷酸变异位点特征,153株深圳本土BA.2.2毒株至少可以分为6条传播链。与特征性突变相比,1株美国输入的受关注BA.2.12.1变异株在N区多了一个P383L氨基酸变异位点。深圳本地与输入的BA.2亚系变异株呈现出了高基因组多样性特征,开展SARS⁃CoV⁃2关切变异株与亚谱系毒株的分子监测,对新型冠状病毒感染(COVID⁃19)疫情的溯源与防控具有重要意义。Severe acute respiratory syndrome⁃coronavirus⁃2(SARS⁃CoV⁃2)Omicron BA.2 and BA.2.12.1 subvariants showed very high transmission capacity.In order to understand the distribution and genetic characteristics of BA.2 sublineages in Shenzhen,China,the whole genome sequence of BA.2 sublineages isolated in Shenzhen,China from January to June in 2022 were analyzed.By using high⁃throughput sequencing,the genome sequences of 185 BA.2 subtype strains with coverage of more than 98%of 155 indigenous and 30 imported strains were obtained.The 185 BA.2 subtypes could be divided into BA.2.2,BA.2.3,BA.2.9,BA.2.10,BA.2.10.1,BA.2.12.1 and BA.2.29 subtypes,among which BA.2.2 accounted with the highest proportion(92.97%,172/185).The proportion of other subtypes from high to low were BA.2.10.1(2.70%,5/185),BA.2.10(1.62%,3/185),BA.2.9(1.08%,2/185),BA.2.3(0.54%,1/185),BA.2.12.1(0.54%,1/185)and BA.2.29(0.54%,1/185).Among 172 BA.2.2 subtype variants,153 strains(88.95%)were native to Shenzhen,China and 19 strains(11.05%)were imported from Hong Kong,China..Sequence analysis showed that 153 BA.2.2 strains from Shenzhen,China and 19 BA.2.2 strains imported from Hong Kong shared 69 nucleotides and 52 amino acid variation(excluding deletion mutations).According to the characteristics of single nucleotide variation sites,the 153 BA.2.2 strains from Shenzhen,China could be divided into at least six transmission chains.Compared with the characteristic mutation,a BA.2.12.1 strain imported from the United States showed an additional P383L amino acid mutation site in the N region.The local and imported BA.2 sublineage variants in Shenzhen,China showed high genomic diversity.Molecular surveillance of SARS⁃CoV⁃2 variants of concern(VOC)and sublineage strains are of great significance for the tracing and prevention and control of COVID⁃19.

关 键 词：新型冠状病毒 BA.2亚系 深圳 基因组序列 溯源 

分 类 号：R373.1[医药卫生—病原生物学]